Sry, that is a terrible argument. You are saying that we do not have to worry about nuclear waste, because we currently do not worry about other waste.
Yeah, but mostly because these applications do not work properly on mobile devices (smaller screen size, too slow, etc.) and a native (in the sense of NOT browser-based) application makes sense. However my hypothesis is just, that the LOOK does not have to fit into the OS.
I think native UIs are overrated and just cause headaches for developers. E.g. take the most popular UI system: HTML/CSS/JS: users have no problem with the fact that all their favourite websites look different.
IMHO it is a better idea when the application enforces the same UI across platforms (like QT) than the platform expecting the same UI for all programs. On top of that QT does support native look&feel.